snATACseq QC with ArchR. Altering LSI parameter: Iteration
Results
QC
ArchR pre-filters the cells using thresholds:
- TSS Enrichment > 4
- Min frags per cell > 1000
Counts
| 510_FC |
7011 |
219 |
141701588 |
15242 |
14.259 |
| 611_FC |
3869 |
161 |
89911016 |
16830 |
11.868 |
| 993_FC |
5273 |
207 |
62967252 |
5871 |
9.037 |
PARAMETER
Iteration : 2
## Warning in kable_pipe(x = structure(c("RNA", "ATAC", "N-undef", "C1", "ExN-1", :
## The table should have a header (column names)

| RNA |
N-undef |
ExN-1 |
RG-1 |
ExN-2 |
InN-3 |
InN-3 |
ExN-4 |
ExN-5 |
ExN-2 |
RG-2 |
RG-1 |
RG-1 |
MG |
InN-1 |
InN-2 |
InN-2 |
| ATAC |
C1 |
C2 |
C3 |
C4 |
C5 |
C6 |
C7 |
C8 |
C9 |
C10 |
C11 |
C12 |
C13 |
C14 |
C15 |
C16 |
Iteration : 4
## Warning in kable_pipe(x = structure(c("RNA", "ATAC", "MG", "C1", "RG-1", : The
## table should have a header (column names)

| RNA |
MG |
RG-1 |
RG-2 |
InN-1 |
InN-2 |
InN-2 |
ExN-4 |
ExN-5 |
InN-3 |
ExN-2 |
InN-3 |
InN-3 |
ExN-5 |
N-undef |
ExN-4 |
RG-1 |
ExN-1 |
| ATAC |
C1 |
C2 |
C3 |
C4 |
C5 |
C6 |
C7 |
C8 |
C9 |
C10 |
C11 |
C12 |
C13 |
C14 |
C15 |
C16 |
C17 |
Iteration : 6
## Warning in kable_pipe(x = structure(c("RNA", "ATAC", "RG-2", "C1", "RG-1", : The
## table should have a header (column names)

| RNA |
RG-2 |
RG-1 |
RG-1 |
MG |
ExN-4 |
ExN-5 |
ExN-3 |
ExN-5 |
ExN-2 |
ExN-2 |
InN-3 |
InN-1 |
InN-2 |
InN-2 |
ExN-1 |
RG-1 |
ExN-1 |
| ATAC |
C1 |
C2 |
C3 |
C4 |
C5 |
C6 |
C7 |
C8 |
C9 |
C10 |
C11 |
C12 |
C13 |
C14 |
C15 |
C16 |
C17 |
Iteration : 8
## Warning in kable_pipe(x = structure(c("RNA", "ATAC", "InN-3", "C1", "ExN-2", :
## The table should have a header (column names)

| RNA |
InN-3 |
ExN-2 |
ExN-4 |
ExN-5 |
N-undef |
ExN-2 |
InN-2 |
ExN-1 |
ExN-2 |
InN-3 |
MG |
InN-1 |
InN-2 |
InN-2 |
RG-2 |
RG-1 |
RG-1 |
| ATAC |
C1 |
C2 |
C3 |
C4 |
C5 |
C6 |
C7 |
C8 |
C9 |
C10 |
C11 |
C12 |
C13 |
C14 |
C15 |
C16 |
C17 |
Iteration : 10
## Warning in kable_pipe(x = structure(c("RNA", "ATAC", "InN-3", "C1", "ExN-1", :
## The table should have a header (column names)

| RNA |
InN-3 |
ExN-1 |
RG-1 |
ExN-3 |
ExN-2 |
InN-3 |
InN-3 |
ExN-4 |
ExN-5 |
ExN-2 |
RG-2 |
RG-1 |
RG-1 |
MG |
InN-1 |
InN-2 |
InN-2 |
| ATAC |
C1 |
C2 |
C3 |
C4 |
C5 |
C6 |
C7 |
C8 |
C9 |
C10 |
C11 |
C12 |
C13 |
C14 |
C15 |
C16 |
C17 |